- phenixbb - phenix-online.org

Reminder: Macromolecular Crystallography - CSHL Course October 2024
by Paul Adams 30 Jul '24

30 Jul '24

Dear Colleagues, We have extended the deadline for the course applications to August 9th. A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 13-29th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. Please follow the link below to the course web site. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road, Cold Spring Harbor, NY 11724 -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Instruct-ERIC Workshop on “Sample Preparation for Single Particle Analysis by Cryo-Electron Microscopy”
by Jose Artur Brito 24 Jul '24

24 Jul '24

Dear Colleagues, We hereby announce a 4-day workshop on "Sample Preparation for Single Particle Analysis by Cryo-Electron Microscopy" [1 [1]]. The course is funded by Instruct-ERIC and will be held at the Iberian Nanotechnology Laboratory (Braga, Portugal), between the 7th and 10th of October this year. The Workshop is aimed primarily at Ph.D students and young Post-Doctoral researchers, is set to provide in-depth training on sample preparation for single particle analysis (SPA) by cryo-electron microscopy (cryo-EM), and is hosted by a team of experts from ITQB NOVA [2 [2]], INL [3 [3]], CNB-CSIC [4 [4]], i3S [5 [5]], and SciLifeLab [6 [6]]. Participants will engage in a comprehensive course featuring a blend of lectures and hands-on tutorials. The lectures will delve into the principles of SPA, covering theoretical and practical aspects of preparing biological samples for negative staining, quality assessment and data collection. The workshop will highlight recent advancements in protein production and stabilization, as well as the latest technological innovations in grid preparation and sample manipulation. Attendees are encouraged to bring their samples, providing a unique opportunity to apply newly acquired skills to their specific research needs. Practical sessions will offer hands-on experience with vitrification using a plunge-freezing device and optimizing grids for sample screening with a cryo-transmission electron microscope (TEM). Participants will be limited to 12 to allow a closer interaction between the participants and the tutors. Candidate selection will be based on a short CV, a motivation letter from the Applicant, and a recommendation letter from the Supervisor. Registration deadline is August 19, 2024, and can be done at the following link: https://www.events.inl.int/instruct-eric-workshop Registration fee is 250Eur for Academics and 500Eur for Non-Academic, and includes accommodation, lunches, coffee-breaks and social dinner. Please feel free to contact us if you have any question. On behalf of the organizing team, hoping to see you in Braga, Jose Artur Brito - ITQB NOVA [1] https://instruct-eric.org/events/16th-instruct-eric-hands-on-workshop-sampl… [2] https://www.itqb.unl.pt/ [3] https://www.inl.int/ [4] http://www.cnb.csic.es/index.php/en [5] https://www.i3s.up.pt/ [6] https://www.scilifelab.se/ -- Links: ------ [1] https://instruct-eric.org/events/16th-instruct-eric-hands-on-workshop-sampl… [2] https://www.itqb.unl.pt/ [3] https://www.inl.int/ [4] http://www.cnb.csic.es/index.php/en [5] https://www.i3s.up.pt/ [6] https://www.scilifelab.se/

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AutoBuild trouble
by Atsushi Nakagawa 17 Jul '24

17 Jul '24

Dear all, I cannot run AutoBuild from GUI both on dev-5383 and 1.21.1. The process terminated with the following message during the process of AutoBuild_multiple_models. Job terminated with at new message window shown below, ********************************************************************************* Failed to carry out AutoBuild_multiple_models: ‘module’ object has no attribute ‘run_autobuild’ ********************************************************************************* Is there any problem on my installation or parameters? AutoBuild runs with the older version (1.20). Thank you for your help. Atsushi

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running phenix
by khkim＠korea.ac.kr 16 Jul '24

16 Jul '24

Dear colleagues, Running phenix received an error (below). Status window indicates "You appear to have another session of PHENIX running already (hostname...), which has locked your project database". I had tried to change project directories. Many thanks. Error in sys.excepthook: Traceback (most recent call last): File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 898, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/Error.py", line 76, in show_exception_dialog if (app.bug_timer.IsRunning() is False): AttributeError: 'PhenixApp' object has no attribute 'bug_timer' Original exception was: Traceback (most recent call last): File "/usr/local/bin/phenix-1.20.1-4487/build/../modules/phenix/wxGUI2/command_line/main.py", line 23, in <module> run(sys.argv[1:]) File "/usr/local/bin/phenix-1.20.1-4487/build/../modules/phenix/wxGUI2/command_line/main.py", line 17, in run wxapp = App.PhenixApp(args) File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 74, in __init__ wx.App.__init__(self, 0) File "/usr/local/bin/phenix-1.20.1-4487/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8628, in __init__ self._BootstrapApp() File "/usr/local/bin/phenix-1.20.1-4487/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8196, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 120, in OnInit self.start_gui() File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 191, in start_gui self.launch_main() File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 507, in launch_main frame = PhenixGUI() File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/Home/Main.py", line 51, in __init__ self.setup_panels() File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/Home/Main.py", line 171, in setup_panels self.refresh_project_list() File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/Home/Main.py", line 360, in refresh_project_list self.add_projects(group_name=current_group) File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/Home/Main.py", line 352, in add_projects group_name=group_name) File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/phenix/tracking/project_db.py", line 72, in get_project_summaries group_id = self.get_group_id_by_name(to_unicode(group_name)) File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/phenix/tracking/project_db.py", line 608, in get_group_id_by_name assert (name in [None, "None", "All", "All groups"]) AssertionError

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Re: [phenixbb] C-beta outliers - it is 1.20 version issue
by Andrea Smith 13 Jul '24

13 Jul '24

Thank you everyone for suggestions. As it turns out, there is a problem in the 1.20 phenix version that I was using. I updated to 1.21 as suggested by Dorothee, repeated one refinement job and had no more C-beta outliers, so I am guessing I will not have them in other models either. Best, Andrea On Friday, June 14, 2024 21:16 CEST, Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: Andrea Can you send me files off-line? Cheers Nigel ---Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated BioimagingLawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : NWMoriarty(a)LBL.govWeb : CCI.LBL.govORCID : orcid.org/0000-0001-8857-9464 On Thu, Jun 13, 2024 at 9:59 AM Andrea Smith <andrea.smith(a)uochb.cas.cz> wrote: Hi all, I am running Phenix v. 1.20.1-4487 on Windows and I keep on getting C-beta outliers of methionine residues after phenix.refine (happened in different data from two different proteins). Even if I correct the methionines in Coot (and they fit perfectly in the density), I get the outliers at the end of refinement again (while these outliers don't fit the density and I can see a green difference map where the C-beta is). Why is this? Is there a way to tell phenix.refine not to move a specific amino acid during refinement? Thanks, Andrea _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org

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refine and Table 1
by Andrea Smith 09 Jul '24

09 Jul '24

Hi everyone, * I have an issue with phenix.refine being unable to open generated pdb and mtz files in coot after refinement. It claims “ERROR: refinement output file not found!” This started happening after I opened the model in ChimeraX and used dssp command and then saved model as pdb that I used for further refinements. The files generated from phenix.refine actually exist, but instead of just being named e.g. myprotein_refine20.pdb they are called myprotein_refine19_refine020.pdb (yes there is an extra refine and an extra 0). This has never happened to me before. * I am also trying to generate "Table 1" for journal. I input my pdb into model file and mtz into reflection file. When I click Run, I get an error message: "a model is referenced in the phil which is not in the data manager". What does this mean? * I also tried to validate my model using pdb validate server, but when I upload cif files generated as output from phenix.refine, the server shows “Error processing uploaded files…Click to reload”. (However, when I use the Get PDB validation report task in phenix, I get a validation report pdf with no issues.) Is all of this caused by the changes the ChimeraX's dssp command did to my pdb? Thank you, Andrea Running Phenix 1.21-5207 from GUI on Ubuntu 20.04.3.

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Re: [phenixbb] refine and Table 1
by Andrea Smith 09 Jul '24

09 Jul '24

Hi Yi Min, my problem number 2 was indeed resolved after I restarted my system. Thank you, Andrea On Tuesday, July 09, 2024 14:47 CEST, Yi Min Ng <yimin_ng(a)outlook.com> wrote: Hi Andrea, I am still new to this field and I have previously came across your #2 problem when trying to generate Table 1 using Phenix. I don't know exactly what was causing the problem but I somehow managed to generate Table 1 after restarting the GUI. You might want to try restarting the software if you haven't tried so? Hope some experts will be able to help you with the problems soon 🤞 Best wishes,Yi Min ______________________________________________________________________________ From: phenixbb-bounces(a)phenix-online.org <phenixbb-bounces(a)phenix-online.org> on behalf of Andrea Smith <andrea.smith(a)uochb.cas.cz> Sent: 09 July 2024 14:25 To: phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> Subject: [phenixbb] refine and Table 1 Hi everyone, * I have an issue with phenix.refine being unable to open generated pdb and mtz files in coot after refinement. It claims “ERROR: refinement output file not found!” This started happening after I opened the model in ChimeraX and used dssp command and then saved model as pdb that I used for further refinements. The files generated from phenix.refine actually exist, but instead of just being named e.g. myprotein_refine20.pdb they are called myprotein_refine19_refine020.pdb (yes there is an extra refine and an extra 0). This has never happened to me before. * I am also trying to generate "Table 1" for journal. I input my pdb into model file and mtz into reflection file. When I click Run, I get an error message: "a model is referenced in the phil which is not in the data manager". What does this mean? * I also tried to validate my model using pdb validate server, but when I upload cif files generated as output from phenix.refine, the server shows “Error processing uploaded files…Click to reload”. (However, when I use the Get PDB validation report task in phenix, I get a validation report pdf with no issues.) Is all of this caused by the changes the ChimeraX's dssp command did to my pdb? Thank you, Andrea Running Phenix 1.21-5207 from GUI on Ubuntu 20.04.3.

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Computations Crystallography Newsletter (CCN) Submissions
by Nigel Moriarty 01 Jul '24

01 Jul '24

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 22 JAN 2024. Please consider writing an article of general interest to the community. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : NWMoriarty(a)LBL.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

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real_space_refine is un-glycosylating my protein
by robert＠oeffner.net 01 Jul '24

01 Jul '24

Hi, I am trying to do a refinement with phenix.real_space_refine (RSR) on an EM map with a protein and a known ligand (NAG is the monomer code). In the pdb file supplied the C1 atom in the NAG molecule is positioned nicely in the EM density at a distance of 1.38Å from a ND2 atom in an ASN residue of the protein. The O1 atom in the NAG molecule is not present suggesting there should be a covalent bond here I believe. Both ASN and the NAG molecule have the same chainID. The problem is that RSR moves the sugar away even though I have used command line options such as pdb_interpretation.automatic_linking.link_carbohydrates=True or even pdb_interpretation.automatic_linking.link_all=True. The atoms end up at an un-bonded distance of 2.85Å from each other after refinement to the point that one of them is poking out of the density. Are my phil parameters incorrect? I noticed that I don't get an error message if I misspell say pdb_interpretation.automatic_linking.link_carbohydrates to pdb_interpretation.automatic_linking.link_carbohydrate. RSR still runs to completion so I'm wondering if it actually interprets the PHIL parameter at all. Another peculiarity is that the log file comments that NAG is an unusual residue rather than stating it is a well-known carbohydrate. If anyone on here knows how to compel phenix RSR into creating automatic links to carbohydrates suggestions would be much appreciated. Many thanks, Rob

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Extra map coefficients in 1.21.1-5286
by Dr. Kevin M Jude 29 Jun '24

29 Jun '24

In my latest installed version of phenix, I find that additional, redundant map coefficients are being added to the output mtz file. I compare an identical refinement originally run in 1.21rc1_5058 and then repeated in 1.21.1-5286. *_filled and *_4 appear to be redundant, and the final sets of coefficients (*_no_fill and *_5), appear to include the test set reflections, even though I’ve selected Exclude R-free set from map coefficients in the gui. This is a little bit confusing, but primarily an annoyance because auto-open mtz in coot can’t figure out which coefficients to use. 1.21rc1_5058 Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 NONE -42 41 0 100.00 -3.3 16.0 52.38 1.96 H H 2 NONE 0 28 0 100.00 10.3 10.3 52.38 1.96 H K 3 NONE 0 27 0 100.00 10.3 10.3 52.38 1.96 H L 4 NONE -94.4 13012.5 269 98.44 85.01 85.49 45.63 1.96 J I-obs 5 NONE 0.2 337.4 269 98.44 4.44 4.44 45.63 1.96 Q SIGI-obs 6 NONE 0.0 1.0 269 98.44 0.05 0.05 45.63 1.96 I R-free-flags 7 NONE 10.2 2509.6 321 98.14 129.94 129.94 36.90 1.96 F F-obs-filtered 8 NONE 1.3 35.8 321 98.14 10.11 10.11 36.90 1.96 Q SIGF-obs-filtered 9 NONE 0.1 2250.2 321 98.14 125.18 125.18 36.90 1.96 F F-model 10 NONE -180.0 180.0 321 98.14 4.35 89.81 36.90 1.96 P PHIF-model 11 NONE 0.0 2971.8 1165 93.23 117.81 117.81 36.90 1.96 F 2FOFCWT 12 NONE -180.0 180.0 1165 93.23 4.65 89.89 36.90 1.96 P PH2FOFCWT 13 NONE 0.0 2971.8 0 100.00 117.93 117.93 52.38 1.96 F 2FOFCWT_filled 14 NONE -180.0 180.0 0 100.00 4.85 90.05 52.38 1.96 P PH2FOFCWT_filled 15 NONE 0.0 738.9 1165 93.23 46.86 46.86 36.90 1.96 F FOFCWT 16 NONE -180.0 180.0 1165 93.23 4.75 90.35 36.90 1.96 P PHFOFCWT 1.21.1-5286 Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 NONE -42 41 0 100.00 -3.3 16.0 52.38 1.96 H H 2 NONE 0 28 0 100.00 10.3 10.3 52.38 1.96 H K 3 NONE 0 27 0 100.00 10.3 10.3 52.38 1.96 H L 4 NONE -94.4 13012.5 269 98.44 85.01 85.49 45.63 1.96 J I-obs 5 NONE 0.2 337.4 269 98.44 4.44 4.44 45.63 1.96 Q SIGI-obs 6 NONE 0.0 1.0 269 98.44 0.05 0.05 45.63 1.96 I R-free-flags 7 NONE 10.3 2535.0 321 98.14 131.25 131.25 36.90 1.96 F F-obs-filtered 8 NONE 1.3 36.1 321 98.14 10.21 10.21 36.90 1.96 Q SIGF-obs-filtered 9 NONE 0.0 2261.4 321 98.14 126.66 126.66 36.90 1.96 F F-model 10 NONE -180.0 180.0 321 98.14 3.96 89.82 36.90 1.96 P PHIF-model 11 NONE 0.0 3119.6 1165 93.23 119.71 119.71 36.90 1.96 F 2FOFCWT_1 12 NONE -180.0 180.0 1165 93.23 4.33 89.89 36.90 1.96 P PH2FOFCWT_1 13 NONE 0.0 3119.6 0 100.00 119.85 119.85 52.38 1.96 F 2FOFCWT_filled 14 NONE -180.0 180.0 0 100.00 4.44 90.05 52.38 1.96 P PH2FOFCWT_filled 15 NONE 0.0 780.4 1165 93.23 45.28 45.28 36.90 1.96 F FOFCWT_2 16 NONE -180.0 180.0 1165 93.23 4.21 90.36 36.90 1.96 P PHFOFCWT_2 17 NONE 0.0 3119.6 0 100.00 119.74 119.74 52.38 1.96 F 2FOFCWT_4 18 NONE -180.0 180.0 0 100.00 4.60 90.01 52.38 1.96 P PH2FOFCWT_4 19 NONE 0.0 3119.6 321 98.14 119.56 119.56 36.90 1.96 F 2FOFCWT_no_fill 20 NONE -180.0 180.0 321 98.14 4.40 89.94 36.90 1.96 P PH2FOFCWT_no_fill 21 NONE 0.0 780.4 321 98.14 45.68 45.68 36.90 1.96 F FOFCWT_5 22 NONE -180.0 180.0 321 98.14 4.12 90.23 36.90 1.96 P PHFOFCWT_5 Best wishes Kevin -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431<tel:%28650%29%20723-6431>

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Postdoctoral Job Position in Infectious disease and Small Angle X-ray Scattering
by Susan Tsutakawa 26 Jun '24

26 Jun '24

Dear fellow structural biologists, I would appreciate it if you could forward this message to any graduate students that might be interested. We have an opening for a Postdoctoral Fellow to use small angle X-ray scattering (SAXS) on global health problems and biopreparedness in response to infectious disease work at the SIBYLS <http://bl1231.als.lbl.gov/> Beamline in the Advanced Light Source Synchrotron (ALS) at Lawrence Berkeley National Laboratory (LBNL) In this exciting role, you will work with a multi-disciplinary team of scientists as part of the ArpaH program <https://arpa-h.gov/>, structurally characterizing purified proteins from pandemic-potential organisms and relevant antibodies. The primary technique used will be Small Angle X-ray Scattering, which provides distance information that can reflect protein conformations and complexes in solution. You will work with a team to develop portable instrumentation to enable high throughput SAXS sample handling that can work at other synchrotrons. Through this work, you will develop ties to other national laboratories and within Berkeley Lab, specifically within the National Energy Research Scientific Computing Center (NERSC <https://www.nersc.gov/>), a division within the Computing Sciences Area’s <https://cs.lbl.gov/>. Prior experience in structural biology, protein biochemistry, and basic programming would be advantageous. Experience in SAXS is not a requirement. For more details. please see https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=102111 This position has an anticipated start date of September 1, 2024. LBNL is located in the San Francisco Area in Berkeley, CA. Sincerely, Susan Tsutakawa Head of Structural Biology Molecular Biophysics and Integrated Bioimaging Biosciences Area Lawrence Berkeley National Laboratory.

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Multiple postdoctoral and Ph.D. positions at IBS (Grenoble)
by Elke De Zitter 26 Jun '24

26 Jun '24

Dear all, We have four immediate openings for postdoctoral researchers and one opening for a Ph.D. student in the DYNAMOP group at the Institute for Structural Biology in Grenoble (France). The first postdoctoral project focuses on the development and optimization of bio-scavengers targeting toxic compounds. The researcher with use time-resolved crystallography and in silico design methodologies. Interested candidates can find more information at [ https://www.ibs.fr/en/careers/job-offers/two-year-postdoctoral-position-for… | https://www.ibs.fr/en/careers/job-offers/two-year-postdoctoral-position-for… ] (application deadline: 12/07/2024 ). In the second postdoctoral project, the researcher will study the binding of toxic compounds to their physiological target and subsequent chemical reactivation via time-resolved crystallography. The third postdoctoral project is focused on the development of an experimental approach for the determination of the photoinduced structural dynamics of photosensitive biomolecules both in vitro and in cell using time-resolved X-ray scattering techniques. More information and the application procedure can be found on [ https://emploi.cnrs.fr/Offres/CDD/UMR5075-VALLAN-024/Default.aspx?lang=EN | https://www.ibs.fr/en/careers/job-offers/two-year-postdoctoral-position-for… ] (application deadline 30/06/2024). In the fourth postdoctoral project, the researcher will apply serial diffraction techniques (SSX, SFX, SED) to structurally study natural and recombinant protein nanocrystals Last, a 3-year funded PhD fellowship is available to explore the structural dynamics of the orange carotenoid protein by means of time-resolved serial crystallography. Applicants for the postdoctoral positions must have obtained a Ph.D. in structural biology, biophysics, biochemistry, physics, chemistry, or a related field. The candidates must show a track-record of publications in peer-reviewed journals. Applicants for the Ph.D. position are expected to have a master's degree in one of the above mentioned fields. All candidates are expected to be proficient in English and highly motivated to learn new skills. The candidates need to be a good team player as well as being capable of working independently. For inquiries regarding the positions and application processes, please contact Elke De Zitter ( [ mailto:[email protected] | elke.de-zitter(a)ibs.fr ] ), Martin Weik ( [ mailto:[email protected] | martin.weik(a)ibs.fr ] ), Giorgio Schiro ( [ mailto:[email protected] | giorgio.schiro(a)ibs.fr ] ) or Jacques-Philippe Colletier ( [ mailto:[email protected] | jacques-philippe.colletier(a)ibs.fr ] ) Best regards, Martin, Giorgio, Jacques-Philippe and Elke Elke De Zitter Institut de Biologie Structurale - IBS group DYNAMOP 71 avenue des Martyrs 38044 Grenoble Cedex 9, France +33 4 57 42 86 56 elke.de-zitter(a)ibs.fr

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Hardware migration
by Billy Poon 18 Jun '24

18 Jun '24

Hi everyone, We are in the process of migrating these bulletin boards to new hardware over the next few weeks. I will make another post once the migration is completed. Nothing will be changed until then. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

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Test post
by Billy Poon 18 Jun '24

18 Jun '24

This is a test message using the new hardware. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

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C-beta outliers
by Andrea Smith 14 Jun '24

14 Jun '24

Hi all, I am running Phenix v. 1.20.1-4487 on Windows and I keep on getting C-beta outliers of methionine residues after phenix.refine (happened in different data from two different proteins). Even if I correct the methionines in Coot (and they fit perfectly in the density), I get the outliers at the end of refinement again (while these outliers don't fit the density and I can see a green difference map where the C-beta is). Why is this? Is there a way to tell phenix.refine not to move a specific amino acid during refinement? Thanks, Andrea

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Help with Phenix/Rosetta Interface Installation
by Lucas Souza 14 Jun '24

14 Jun '24

Dear all, I have been trying to install rosetta (both release 371 and 20221.16.61629)/phenix (1.21.1-5286) interface in Ubuntu 24.04, but with no success at all. Both Rosetta installation and "rosetta.build_phenix_interface" ends up with no erros. But, when I run "rosetta.run_tests" or try to "phenix.rosetta_refine" I always get the error below: ------- /Generating 2 models on 1 processors... / /DEBUG dumping error message ERROR: Rosetta exited with status 139 stderr output: AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS. Segmentation fault (core dumped) Traceback (most recent call last): File "/home/lucas/pckg/phenix-1.21.1-5286/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 315, in <module> run(sys.argv[1:], create_dir=True) File "/home/lucas/pckg/phenix-1.21.1-5286/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 198, in run debug=params.output.debug) File "/home/lucas/pckg/phenix-1.21.1-5286/modules/phenix/phenix/rosetta/refine.py", line 329, in __init__ self.run_jobs() File "/home/lucas/pckg/phenix-1.21.1-5286/modules/phenix/phenix/rosetta/refine.py", line 403, in run_jobs check_result(result) File "/home/lucas/pckg/phenix-1.21.1-5286/modules/phenix/phenix/rosetta/refine.py", line 394, in check_result raise RuntimeError("Aborted due to error in job %d." % result.job_id) RuntimeError: Aborted due to error in job 1./ /Something tells me this is related to the drop of support to Python2 in the new Ubuntu release, but I could not figure out what exactly is the issue. I uploaded both stdout and ROSETTA_CRASH.log in this email./ ------- If anyone can help me with this issue, I would be very happy. Thank you all! Lucas

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(IUCr) The evolution of raw data archiving and the growth of its importance in crystallography
by John R Helliwell 12 Jun '24

12 Jun '24

Dear Colleagues, Our article on this topic, which I imagine will be of keen interest, published this afternoon, is available open access from this weblink:- https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html Best wishes, John Emeritus Professor John R Helliwell DSc

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ADP-BEF-link.cif
by Heidi Schubert 10 Jun '24

10 Jun '24

Hi AAA ATPase modelers Could anyone send me the .cif file to define the link between ADP and a BeFx ion? I’m hoping this has not only the revised angle/bond info between O3B and Be but also the new angle between the Be and Fs different from the planar simple ion. AND, for my hexamer I assume the apply_link.def file then just reads with repetitive 5-line groups: refinement.pdb_interpretation.apply_cif_link { data_link = ADP-BEF residue_selection_1 = chain A and resname ADP and resseq 901 residue_selection_2 = chain A and resname BEF and resseq 902 } Where I change out the chain name but keep calling them residues_selection1 and 2? Many thanks Heidi Heidi Schubert Research Professor Department of Biochemistry University of Utah Rm 116 BPRB 20 S 2030 E Salt Lake City, UT 84112 heidi(a)biochem.utah.edu<mailto:[email protected]> 801-585-9776

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high and low resolution in Phenix 1.21.1-5286-000
by Dominik Oberthuer 30 May '24

30 May '24

Hi, because of an update to Sonoma, I also had to update to Phenix 1.21.1-5286-000. When I'm running phenix.refine from the GUI, use an MTZ with resolution e.g. from 1.65 - 51A, use "High resolution" and "Low resolution" to refine against a specific range of data, phenix.refine does not cut off the data beyond the limits set there, but instead takes all of the data. For sure, I cut the MTZ before, but many times it is about trying out which data to include and not include and this is not really how it should be... Is this known? Is there any way to solve this issue? Thanks! Dominik -- Dr. Dominik Oberthür CFEL - Center for Free-Electron Laser Science - DESY Coherent Imaging Division Notkestrasse 85 22607 Hamburg Germany phone: +49 (0)40 8998 6394 dominik.oberthuer(a)cfel.de

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NIGMS Mature Synchrotron Program Evaluation
by Paul Adams 20 May '24

20 May '24

Dear Colleagues, Apologies for the US-centric posting, but I think this is of interest to many of the bulletin board subscribers who make use of synchrotron facilities in the US. NIH is seeking feedback on the Mature Synchrotron Program: https://grants.nih.gov/grants/guide/notice-files/NOT-GM-24-019.html This program supports synchrotron-based user resources where the technologies are at an advanced level, including Macromolecular Crystallography, Small-Angle and Wide-Angle X-ray Scattering, fiber diffraction, and other synchrotron-based techniques that generate important data, with an emphasis on structural biology. Responses to the RFI will be accepted through 6/17/2024. All comments will be anonymous and should be submitted electronically via a web form at: https://www.research.net/r/P30_RFI As the Director of one of the resources it has been suggested that I help make the community aware of the RFI, so there is the opportunity to provide feedback in a timely manner. Feel free to pass this on to any of your colleagues who may be interested. Cheers, Paul -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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"<" symbol in reflection mmcif status column
by Kreitler, Dale 17 May '24

17 May '24

Looking at some output reflection cif files from phenix.refine I'm wondering what does "<" mean in the status column and why would F_calc_with_sovlent structure factors also be missing for these reflections? In some cases I can see it coincides with unobserved reflections, but this doesn't seem consistent. Any insight or links to documentation that describe these values would be much appreciated. Thank you, Dale loop_ _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT _refln.pdbx_r_free_flag _refln.status _refln.pdbx_F_calc_with_solvent _refln.pdbx_phase_calc_with_solvent ... 30 0 48 65.2227 18.9183 72.4766 0 5.77152 -2.25565e-14 3 o 77.6435 1.95165e-15 30 0 49 206.068 7.45891 200.645 120 ? ? 19 < ? ? 30 0 50 33.324 17.5773 1.10423 -120 0.328059 -120 10 o 0.916822 -120 30 0 51 23.7705 14.8724 10.7438 180 2.40893 1.88332e-14 6 o 16.3173 180 ... 32 7 2 ? ? 11.4163 118.276 ? ? 5 < ? ? 32 7 3 ? ? 52.373 -121.74 ? ? 10 < ? ? 32 7 4 ? ? 33.1269 -26.1149 ? ? 3 < ? ? 32 7 5 ? ? 106.054 -86.2146 ? ? 19 < ? ? ============================= Dale Kreitler AMX Beamline Scientist National Synchrotron Light Source II Building 745, Rm. 5L143 Upton, NY 11973 631-344-7318

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ADP refinement in phenix.real _space_refine
by Luca Pellegrini 16 May '24

16 May '24

While refining a protein-DNA complex in a cryoEM map (~2.5-7A), I have noticed the following behaviour of ADP refinement: - If NCS is on for the protein chains, no ADP refinement of the DNA takes place. - If NCS is off, ADP refinement behaves oddly: one strand of dsDNA is refined with atomic ADPs, the other strand with group ADPs (one per nucleotide). The group ADPs take up unphysical values (lower ADPs in poor map regions), whereas the atomic ADPs look sensible. - To get the ADP refinement of DNA to behave normally, I need to both leave NCS out and set nproc=1 explicitly (haven’t tried other values). I wonder if any of this has been seen before or am I not doing this correctly? Phenix-dev-5330 iMac, Catalina 10.15.7, 8-core Intel i9 Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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ligand links
by Heidi Schubert 14 May '24

14 May '24

Hi, Do you think you can link one ligand to two other molecules. (one NON-POLYMER and one peptide). I guess my other option is to create a new ligand. I assumed you pre-deleted the atoms that are supposed to be deleted in the link? I did delete them and it complained and I put them back in and it’s complaining. Pretty similar errors, but I’m wondering if it’s just the second link that’s causing problems. I’ve got files PNS.cif ACE.cif PNS-SER.cif ACE-PNS.cif apply_link_ACE-PNS.def apply_link_PNS-SER.def Heidi [A screenshot of a computer error Description automatically generated]

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Error upon Phenix installation - Manjaro WSL2
by Nicolas Caramello 03 May '24

03 May '24

Dear PhenixBBers, I call upon your wisdom because I recently tried to install Phenix 1.20 on a windows subsystem for linux distribution of Manjaro (Archlinux based) and have failed with the following error : ========================================================================== Phenix Installation version: 1.20.1-4487 machine type: intel-linux-2.6-x86_64 OS version: 5.15.146.1-microsoft-standard-WSL2 destination: /home/my_machine/phenix-1.20.1-4487 # of processors: 20 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 268, in <module> installer(sys.argv[1:]).install() File "/home/my_machine/phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 200, in install self.install_from_binary() File "/home/my_machine/phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 349, in install_from_binary self.reconfigure(log=log) File "/home/my_machine/phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 431, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/home/my_machine/phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 55, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/home/my_machine/phenix-1.20.1-4487/conda_base/bin/python /home/my_machine/phenix-1.20.1-4487/modules/cctbx_project/libtbx/configure.py --current_working_directory /home/my_machine/phenix-1.20.1-4487/build --command_version_suffix 1.20.1-4487 phenix phaser phasertng solve_resolve labelit dials xia2 iota prime amber_adaptbx --use_conda' failed with exit code 127 Trying to install Phenix 1.21 has produced the same error. I have not managed to solve this, regardless of whether I was running the installation command with sudo privileges or as root. For context, I successfully installed Phenix 1.20 on the same machine and same distribution 6 months ago, but had to reinstall everything since and it does not work anymore now. Have you heard of such an error? Do you have a hint on how to fix it? Best regards, Nicolas Caramello PhD student Structural Biology Group - ESRF /Institut für Nanostruktur/- /und/ Festkörperphysik- Universität Hamburg

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ccp4 thread: "what happened to Molprobity"
by Pavel Afonine 01 May '24

01 May '24

Hi All, I hope someone from Molprobity end reads CCP4 mailing list where people report issues with Molprobity (server and from within Phenix). Just in case this needs someone's attention. Pavel

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on the criteria for outliers, phenix.molprobity and wwPDB validation
by Jorge Iulek 29 Apr '24

29 Apr '24

Hi all, I had already noticed that outliers spotted by phenix with its validation tool, with the nice feature to carry one straight to the "suspicious" residue in a coot session for visual inspection, differs a bit from what comes spotted from wwPDB validation, generally the latter spotting some few more residues. To one current structure, which at low resolution, I notice there is a bit larger difference between the number of spotted residues. I see from wwPDB validation, molprobity is also used to spot outliers for many of the analyses. I see the current molprobity version used is 4.02b-467, but I could not yet devise the molprobity version used by phenix. Of course, there would also be the "library" used in each case to spot the outliers. Maybe someone ever listed what is considered in each case, and their differences, or a link to that is welcome for me. What would be the best criteria for spotting is of course a good discussion. But a superficial question I would make is if there is a way to make phenix.molprobity output to resemble the one from wwPDB validation, at least the ones accounted by molprobity? Jorge

2 2

Phenix resolve_cryo_em with local resolution
by Reza Khayat 29 Apr '24

29 Apr '24

Hi, Is it possible to run resolve_cryo_em and have it consider the local resolution of the two half maps in the final map? I have a 3.7Angstrom map were certain domains, too small for local refinement with single particle analysis, are smeared out in the resolve_cryo_em map. Their densities are stronger when I low pass filter the original maps. The adjust_local_resolution_coloring = True option seems to be what I need; however, including this option in the command line results in: Please run this program with the --show-defaults option to see what parameters are available. PHIL parameters in files should be fully specified (e.g. "output.overwrite" instead of just "overwrite") The command line I use is: phenix.resolve_cryo_em map_file_name=Class001_full_box_40.ccp4 half_map_file_name_1=Class001_half1_box_40.ccp4 half_map_file_name_2=Class001_half2_box_40.ccp4 resolution=4.0 dm_resolution=3.5 cycles=1 box_before_analysis=False density_modify_unsharpened_maps=True nproc=16 force_nproc=True model_1=Class001.pdb seq_file=Class001.fasta ncs_copies=1 output_directory="Class001_local" adjust_local_resolution_coloring=True > Class001_local.log Any help would be appreciated. Thanks. Best wishes, Reza Reza Khayat, PhD City College of New York Associate Professor Department of Chemistry and Biochemistry Co-Director NIH G-RISE program

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chain name lentgh
by Roberto Marabini 18 Apr '24

18 Apr '24

Hi, We are using phenix version 1.20.1-4487. The protein complex we are processing has more than 100 chains. For this complex we would like to use chain names longer than 2 characters but I see that phenix output truncates the names to the last two characters. Is there any way to avoid this constraint, that is, can we get output files with longer chain names? thanks for the help Roberto

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change sigma for an already restrained bond
by Jorge Iulek 18 Apr '24

18 Apr '24

Dear all, I would like to change the sigma value for an already restrained bond. I enter for phenix.refine: " bond { action = add delete *change atom_selection_1 = chain D and resid 493 and name CA atom_selection_2 = chain D and resid 493 and name CB symmetry_operation = None distance_ideal = 1.532 sigma = 1.02e-2 slack = None limit = -1.0 top_out = False } " In the log I get: " ... Custom bonds: bond: atom 1: "ATOM 14355 CA ALA D 493 .*. C " atom 2: "ATOM 14358 CB ALA D 493 .*. C " symmetry operation: x,y,z distance_model: 1.511 distance_ideal: 1.532 ideal - model: 0.021 slack: 0.000 delta_slack: 0.021 sigma: 0.0102 Total number of added/changed bonds: 1 ... " But in the .geo file I read: " User supplied restraints: 1 Sorted by residual: bond pdb=" CA ALA D 493 " pdb=" CB ALA D 493 " ideal model delta sigma weight residual 1.532 1.511 0.022 1.28e-02 6.10e+03 2.85e+00 " 1.28e-02 is the default value. On the other hand, sigma changes for angles and dihedrals seem to work as expected (the intended values are echoed to the .geo file). To add up, if a bond is *added*, the value is in the .geo file. I observe this for both 1.20.1-4487 1.21-5207 versions. So, in short, should I be allowed to *change the sigma* for a specific *bond*? How should I do it? Thanks Jorge

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iNEXT/3D-Bioinfo AI in structural biology workshop announcement
by Jon Agirre 15 Apr '24

15 Apr '24

Dear all, It is our pleasure to announce the joint iNEXT-Discovery and 3D-Bioinfo workshop on "AI advances in structural biology and drug discovery", to be held in Grenoble on 13-14 May 2024. The rapid advancements in Artificial Intelligence (AI) and Machine Learning (ML) have opened up new horizons in the field of Structural Biology and Drug Discovery. This workshop is addressed to scientists in industry and academia, and aims to bridge the gap between the recent developments in AI technologies and experimental approaches in translational research. From understanding biological structures to accelerating the drug discovery processes, participants will gain insights into the latest AI models, as well as high throughput experimental techniques. Through a series of invited and selected talks (abstract submission will remain open until 25 April 2024), attendees will explore the power of combining AI and experimental approaches in translational research. Abstracts will be considered for oral and poster presentations. Please register and send your abstract before 25 April 2024. Website: https://instruct-eric.org/events/ai-approaches-in-structural-biology-and-dr… Registration fee: £50 (includes catering) Venue: EPN campus, Grenoble, France. Dates: 13-14 May 2024 Best regards, Jon Agirre, on behalf of the organising committee: Jose A. Marquez (Instruct-ERIC), Magalie Matthieu (Sanofi-Aventis), Rebecca Thompson (ThermoFisher), Max Nanao (ESRF), Carlos Oscar Sorzano (Instruct-ERIC), Jon Agirre (Instruct-ERIC/3D-Bioinfo liaison), Sameer Velankar (EMBL-EBI, 3D-Bioinfo), Evangelia Chrysina (ICB-NHRF, Greece). -- Dr Jon Agirre Royal Society University Research Fellow (assistant professor) Main editor at Acta Crystallographica Section F: Structural Biology Communications CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir) York Structural Biology Laboratory, Department of Chemistry University of York, Heslington, YO10 5DD, York, UK

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Phenix version 1.21.1 released
by Paul Adams 09 Apr '24

09 Apr '24

The Phenix developers are pleased to announce that version 1.21.1 of Phenix is now available (build 1.21.1-5286). Binary installers for Linux, Mac OSX, and Windows (under Windows Subsystem for Linux), and the source installer, are available at the download site: http://phenix-online.org/download Highlights for this bug fix 1.21.1 version of Phenix include: - Added support for joint X-ray/neutron refinement to phenix.refine GUI - Fixed DMSO restraint - Fixed excessive printing when processing PAE matrix file - Added tutorial for low resolution restraints - Bugfix for LigandPipeline - Bugfix for PredictAndBuild - New program - phenix.renumber_fab: renumber FAB chains using Kabat, Chothia or Martin conventions Please note that this publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Partial occupancy refinement of overlapping inhibitor+water sites
by Matt Jordan McLeod 18 Mar '24

18 Mar '24

Hi all, I am trying to navigate phenix.refine to occupancy refine a partially occupied inhibitor vs. the waters that it displaces. For instance I have molecule resseq 802 in chain A, and waters 1-6 in chain W that are overlapping. When just refining occupancy of the molecule there are clear sites for the waters. How can I refine both of them together so that I can get an occupancy of the molecule vs the group of waters (which should have nearly identical occupancies)? Maybe, a bit more information on the differences in refinement strategy for the occupancy vs fix occupancy vs group occupancy would be more broadly helpful. I tried to make them all a group, but that didn't work as the refinement pushed the waters out and reduced their occupancies to ~0 while leaving the small molecule occupancy about the same as without water. [cid:2b35e3b8-08e5-44ae-9b70-8fdcff613f1a] *Waters are only placed, they are not refined), small molecule is refined to 0.71 occupancy.* -- Matthew Jordan McLeod, PhD Post-Doctoral Fellow | Thorne Lab Cornell University G11 Physical Sciences Building 142 Sciences Drive Ithaca, NY 14853-3501 (607) 279 9382

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uniq segid problem
by jp d 14 Mar '24

14 Mar '24

hi, phenix is crashing with "segid is not unique" problems i have an old job that ran fine in 1.20, in 1.21-5207 i get this (same job script) Sorry: residue.id_str(suppress_segid=false): segid is not unique: pdbres="ALA 65 " segid="PPP " i think the appropriate place in the log is this: Chain: " " Number of atoms: 41993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32612 Duplicate atoms: {' A,C1*': 112, ' A,C2': 112, ' A,C2*': 112, ' A,C3*': 112, ' A,C4': 112, ' A,C4*': 112, ' A, C5': 112, ' A,C5*': 112, ' A,C6': 112, ' A,C8': 112, ' A,N1': 112, ' A,N3': 112, ' A,N6': 112, ' A,N7': 112, ' A,N9': 1 12, ' A,O1P': 112, ' A,O2*': 112, ' A,O2P': 112, ' A,O3*': 112, ' A,O4*': 112, ' A,O5*': 112, ' A,P': 112, ' C,C1*': 71 , ' C,C2': 71, ' C,C2*': 71, ' C,C3*': 71, ' C,C4': 71, ' C,C4*': 71, ' C,C5': 71, ' C,C5*': 71, ' C,C6': 71, ' C,N1': 71, ' C,N3': 71, ' C,N4': 71, ' C,O1P': 71, ' C,O2': 71, ' C,O2*': 71, ' C,O2P': 71, ' C,O3*': 71, ' C,O4*': 71, ' C, O5*': 71, ' C,P': 71, ' G,C1*': 179, ' G,C2': 179, ' G,C2*': 179, ' G,C3*': 179, ' G,C4': 179, ' G,C4*': 179, ' G,C5': 179, ' G,C5*': 179, ' G,C6': 179, ' G,C8': 179, ' G,N1': 179, ' G,N2': 179, ' G,N3': 179, ' G,N7': 179, ' G,N9': 179, ' G,O1P': 179, ' G,O2*': 179, ' G,O2P': 179, ' G,O3*': 179, ' G,O4*': 179, ' G,O5*': 179, ' G,O6': 179, ' G,P': 179, ' U,C1*': 69, ' U,C2': 69, ' U,C2*': 69, ' U,C3*': 69, ' U,C4': 69, ' U,C4*': 69, ' U,C5': 69, ' U,C5*': 69, ' U,C6': 69, ' U,N1': 69, ' U,N3': 69, ' U,O1P': 69, ' U,O2': 69, ' U,O2*': 69, ' U,O2P': 69, ' U,O3*': 69, ' U,O4': 69, ' U,O4*': 69, ' U,O5*': 69, ' U,P': 69} Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 82, 'rna2p_pyr': 63, 'rna3p': 10, 'rna3p_pur': 497, 'rna3p_pyr': 444} Link IDs: {'rna2p': 146, 'rna3p': 1372} the 1.20 log does not have these messages and finished normally. maybe a wildcard problem with those stars ? we are not using the '*' in our files has anyone seen that ? should i go back to 1.20 ? or force it to use the 1.20 chem data lib ? thanks jpd

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red blobs
by Andrea Smith 14 Mar '24

14 Mar '24

Hi, i am working on a structure where I have a few relatively big red blobs (please see attached print screens with maps at 1.2 and 3.5 rmsd). The data were processed at BESSY, mtz was used in Phaser and refined in phenix.refine. Can someone explain why this happens (and whether it is an issue)? Thank you, Andrea

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Two-year postdoctoral position in time-resolved crystallography at IBS in Grenoble
by Elke De Zitter 13 Mar '24

13 Mar '24

Dear all, We have an immediate opening for a two-year postdoctoral researcher in SNaX team of the DYNAMOP group at the Institute for Structural Biology in Grenoble (France). The project focuses on the development and optimization of bio-scavengers targeting toxic organophosphorus compounds. The successful candidate will employ time-resolved crystallography and in silico protein design methodologies. The 2-year postdoctoral position is funded by the French National Research Agency via the University Grenoble Alpes, and is open for a young researcher. Applicants must have obtained a Ph.D. in structural biology, biochemistry, biophysics, physics, chemistry, or a related field, no more than three years before the start of the project. The candidate must show a track-record of publications in peer-reviewed journals, and is expected to be proficient in English and highly motivated to learn new skills. The candidate needs to be a good team player as well as being capable of working independently. Experience with one or more of the following skills would be highly evaluated: protein design or the usage of artificial intelligence for structural biology, protein expression and purification, protein crystallization and macromolecular crystallography, serial crystallography, programming or scripting. Interested candidates should apply through the University Grenoble Alpes job portal at https://emploi.univ-grenoble-alpes.fr/job-offers/postdoctoral-researcher-in… (application deadline: 02/04/2024 ). For inquiries regarding the position and application process, please contact Elke De Zitter at elke.de-zitter(a)ibs.fr . All the best, Elke Elke De Zitter Institut de Biologie Structurale - IBS group DYNAMOP 71 avenue des Martyrs 38044 Grenoble Cedex 9, France +33 4 57 42 86 56 elke.de-zitter(a)ibs.fr

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EMBO Workshop on Molecular Neurobiology, 13th to 17th May 2024, Crete
by Jonathan Elegheert 11 Mar '24

11 Mar '24

Dear all, I would like to bring to your attention the EMBO Workshop on Molecular Neurobiology (https://meetings.embo.org/event/24-mol-neurobiology), which will be held from 13th to 17th May 2024 on the beautiful Greek island of Crete, at the Fodele Beach resort (https://www.fodelebeach.gr/). This is a workshop covering the latest breakthroughs in structural biology, biophysics, imaging, and biological models in neurobiology. Given its cross-disciplinary nature, this EMBO workshop presents a broad overview of the field and an insight into the latest technologies and results. It provides a space for learning, for forging new collaborations, and for presenting ideas that will contribute to the future of molecular neurobiology. The workshop also presents an excellent opportunity for early-career scientists to present their work, with a large number of talks that will be selected from submitted abstracts. The workshop poster is attached to this mail, and more information, as well as the registration links, can be found on the following web page; https://meetings.embo.org/event/24-mol-neurobiology The abstract submission deadline is 6th of March. Please do not hesitate to contact me directly for any questions, and we hope to see many of you there! Best wishes, on behalf of the organising committee, Jonathan ----------------------------------------------------------------- Jonathan Elegheert, PhD Team Leader CNRS Scientist Interdisciplinary Institute for NeuroScience (IINS) <https://www.iins.u-bordeaux.fr/> UMR5297 CNRS / UB Centre Broca Nouvelle-Aquitaine 146 rue Léo Saignat BP 61292 33076 Bordeaux Cedex <https://goo.gl/maps/CFNm4dUvzrmmHUM1A> France T: +33 (0)5 33 51 48 57 E: jonathan.elegheert(a)u-bordeaux.fr W: https://www.iins.u-bordeaux.fr/ELEGHEERT Twitter: @ElegheertLab <https://twitter.com/ElegheertLab> -----------------------------------------------------------------

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Issue phenix.table1 macOS
by Xavier Brazzolotto 09 Mar '24

09 Mar '24

I am facing a strange issue with phenix.table1 Previously, I had generated a Table1 with the GUI that was ok. Recently, I have updated to Sonoma 14.4 and when I try to rerun phenix.table1 (or use similar model and with same reflections) do not get consistent results, especially in number of reflections, uniques, CC1/2, CC*... Besides, at the end of a refinement, I do also get an error when the program tries to auto-load the data (model and maps) in Coot… Any thoughts about this Xavier

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Macromolecular Crystallography - CSHL Course October 2024
by Paul Adams 06 Mar '24

06 Mar '24

Dear Colleagues, The Cold Spring Harbor Macromolecular Crystallography course will take place October 13-29th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. Please follow the link below to the course web site. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> Macromolecular Crystallography <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> October 13 - 29, 2024 Applications Due: July 15 Instructors Paul Adams, Lawrence Berkeley National Laboratory Dorothee Liebschner, Lawrence Berkeley National Laboratory Janet Newman, UNSW, Australia James Pflugrath, Rigaku Americas Corporation (ret.), Texas Co-Instructor Tom Peat, UNSW, Australia Topics Covered Basic Diffraction Theory Structure Presentation Coordinate Deposition Structure Validation Model Building and Refinement Electron Density Maps Improvement Using Predicted Models in Structure Solution and Completion Protein Structure Prediction Structure Solution by Experimental Phasing Methods (SAD, MAD, MIR, and others) and Molecular Replacement Data Collection and Processing Synchrotron X-ray Sources and Optics Crystallization (Proteins, Nucleic Acids, Complexes and Membrane Proteins) For further information and to apply please visit the Macromolecular Crystallography course website. <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road, Cold Spring Harbor, NY 11724 -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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map display after resolve_cryoem
by Valerie Biou 01 Mar '24

01 Mar '24

Hello, I ran resolve_cryoem for solvent flattening and obtained a ccp4 map that behaves like a mask both in Coot and Chimera. the histogram is just a single line and the dimensions are different from my original map, even though in a second run I used restore_full_size = true in a second run. To be clear, my original map has 480^3 dimensions, and the output one is 125x140x224, which boxes my protein but I can't see the inside of the map. I guess there is something I didn't understand. Can you please help me? All the best, Valerie Valérie Biou, Ph.D. valerie.biou(a)ibpc.fr Laboratoire de Biologie Physico-Chimique des Protéines Membranaires umr7099.ibpc.fr <http://umr7099.ibpc.fr/> UMR 7099 CNRS/Univ. Paris-Cité Institut de Biologie Physico-Chimique 13 rue Pierre et Marie Curie 75005 Paris - France Tel : +33 (0)1 5841 5099

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Re: [phenixbb] Joint X-ray / neutron refinement
by Kristoffer Lundgren 24 Feb '24

24 Feb '24

Hello phenixbb, When trying to do joint refinement in phenix.refine 1.21-5207 using the suggested joint_xn.eff file found at https://phenix-online.org/documentation/reference/refinement.html#neutron-a… as a template I get some error messages (running phenix.refine from the command line): Unrecognized PHIL parameters: ----------------------------- xray.refinement.refine.strategy (file "joint_xn.eff", line 33) xray.refinement.main.simulated_annealing (file "joint_xn.eff", line 36) xray.refinement.main.ordered_solvent (file "joint_xn.eff", line 37) xray.refinement.main.number_of_macro_cycles (file "joint_xn.eff", line 38) neutron.refinement.refine.strategy (file "joint_xn.eff", line 45) neutron.refinement.main.simulated_annealing (file "joint_xn.eff", line 48) neutron.refinement.main.ordered_solvent (file "joint_xn.eff", line 49) neutron.refinement.main.number_of_macro_cycles (file "joint_xn.eff", line 50) Can you please advice on how to proceed? It looks like the options supplied are not recognized at all by phenix.refine. Best regards Kristoffer From: <phenixbb-bounces(a)phenix-online.org> on behalf of Derek Logan <derek.logan(a)biochemistry.lu.se> Date: Monday, 22 January 2024 at 09:39 To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Cc: Ulf Ryde <ulf.ryde(a)compchem.lu.se>, "esko.oksanen_ess.eu" <esko.oksanen(a)ess.eu> Subject: ***SPAM*** [phenixbb] Joint X-ray / neutron refinement Hi phenixbb, I'm trying to understand the current status of joint X-ray/neutron refinement in phenix.refine. The announcement of the latest release mentions a change in the algorithm as described in the recent publication. In the documentation: Structure refinement in PHENIX<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> phenix-online.org<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> [AURqZhI53yp3gAAAABJRU5ErkJggg==]<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> it's described how you can run joint refinement using a parameter file. Does this mean that it is *only* possible in this way and not through the GUI? The GUI was very useful in the past as it automatically opened Coot with the maps for both X-rays and neutrons, and the refinement statistics for both were displayed in the GUI. As far as I can see joint refinement via the GUI last worked in version 1.19.2-4148 from 2021. Best regards Derek

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Rotamer error in real space refinement
by Nikos Pinotsis 23 Feb '24

23 Feb '24

Hi, I am using real space refine with the latest phenix 1.21-5207 for fitting a model into a cryoEM map. During refiment one Trp goes clearly out of density (vertical to the density) although the map is very well defined at this part of the protein. I tried local_grid_search either for every cycle or last, however it didn't fix the problem. I know that this is reported a couple of years ago as fixed (dev-4218), I am wondering if something changed during the last version. Another solution I can think it to keep the side chain of this Trp fixed. How can I do that? thanks Nikos -- ________________________________________ Nikos Pinotsis Associate Professor Biochemistry, Department of Chemistry National and Kapodistrian University of Athens

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Define bond between O3' of a nucleotide to P of 3DR HETATM ligand (abasic nucleotide)
by Mark Saper 23 Feb '24

23 Feb '24

I need to create a phosphodiester bond between O3’ of a DNA nucleotide and P of a 3DR HETATM ligand (a modified nucleotide). I also need to delete O3P of the 3DR nucleotide. How can I create this restraint? Also, how can I get COOT to display this bond? Thanks, Mark _____________________ Mark A. Saper, Ph.D. Dept of Microbiology and Molecular Genetics Hebrew University Faculty of Medicine saper(a)umich.edu <mailto:[email protected]> | +972 52 815-0480

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Tenure track position in Protein Science for Pathogen Defense
by Cygler, Miroslaw 20 Feb '24

20 Feb '24

Dear Colleagues, I am excited to let you know that the Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, is searching for an exceptional candidate in the area of Protein Science for Pathogen Defense, to fill a tenure-track Canada Research Chair (CRC) Tier 2 position. The CRC program is the flagship of a national strategy to make Canada one of the world's top countries in research and development. We are looking for an outstanding early career scientist to establish and lead a groundbreaking research program in protein science to understand the mechanisms of bacterial and viral infection in humans or animals, to investigate host-pathogen interactions, or to discover novel mechanisms of defense against known and potential future pathogens. Within this broad scope, specific areas of interest include synthetic antigen design, the molecular basis of immune response to pathogens, mechanisms of antimicrobial resistance, and the prediction-guided design of artificial antibodies. We are interested in hiring a world-class expert in one or more of the following areas: (i) protein structure prediction and structural bioinformatics, (ii) protein design, and (iii) cryo-electron microscopy. A detailed advertisement with instruction how to apply is enclosed and can also be viewed here: <https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> Canada Research Chair (CRC) Tier 2 in Protein Science for Pathogen Defense<https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> protection.outlook.com<https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> [X]<https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> . Regards, Mirek ======================================================= Dr. Miroslaw Cygler, FCAHS Professor, Dept. Biochem, Microbiol & Immune, U. of Saskatchewan Canada Research Chair in Molecular Medicine Using Synchrotron Light Health Sciences Building 3D30.6 (Box 9) 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada Email: miroslaw.cygler(a)usask.ca<mailto:[email protected]> Website: http://research-groups.usask.ca/cyglerlab/ Phone: 306-966-4361, cell: 306-203-2317 =======================================================

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Structural Biology Workshop, June 10-12, 2024, Arlington, VA
by Meilleur, Flora 15 Feb '24

15 Feb '24

Dear All, We would like to bring to your attention the 2024 Neutrons in Structural Biology workshop. This workshop will highlight the need for next-generation instruments and toolsets for structural biology, with a focus on neutrons and other complementary techniques, and the development of integrated experimental and computational frameworks that connect them. Neutrons in Structural Biology - Challenges & Opportunities June 10-12th 2024 Sheraton Pentagon City Hotel, Arlington, VA. For details and registration see: Neutrons in Structural Biology - Challenges & Opportunities<https://conference.sns.gov/event/402/> The workshop will include a 1-day satellite training workshop (June 10, 2024) to educate graduate students and postdoctoral researchers in the application of neutron techniques in structural biology. A limited numbers of travel awards are available to support graduate students and post-doctoral fellows attendance at the workshop. The travel award application deadline is April 12, 2024. Details here<https://conference.sns.gov/event/402/page/2891-travel-awards-deadline-april…>. Flora Meilleur on behalf of the organizing committee: Andrey Kovalevsky Flora Meilleur Dean Myles Hugh O'Neill Flora Meilleur, Ph.D. Neutron Scattering Scientist Neutron Sciences Directorate Oak Ridge National Laboratory Professor Molecular & Structural Biochemistry N C State University Editor, Journal of Applied Crystallography Office: 865-576-2779

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to leave atoms out of ADP restraints
by Jorge Iulek 13 Feb '24

13 Feb '24

Hi, all, The ADP restraints I refer to in this discussion are the ones that would make B-factors of nearby atoms to influence (or more or less resemble) each other. For some very disordered side chains, I would like to test "taking out" the "more disordered" atoms (maybe for high chi angle variability) of these restraints, for them to be more free to skyrocket, but also that they do not influence so much the main chain, in some cases where the flexibility difference between main and side chain seems to be significant. Is there a way to do so? Thanks, Jorge

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helical structure - Real space refinement
by Dmitry Semchonok 01 Feb '24

01 Feb '24

Dear colleagues, Is there any specific procedure for Real space refinement in Phenix, having a map and model when working with helical structure? Many thanks Kind regard, Dmitry

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RealSpaceRefine Nucleic acid SS restraints ?
by CUNIASSE Philippe 31 Jan '24

31 Jan '24

Dear all, I am currently refining a protein-nucleic acid structure obtained by MDFF (NAMD) with a 2.9 Å cryo-EM map. Dues to the poor density of the map at the end of the DNA duplex (likely due to breathing at the ends of the duplex), the structure of the DNA tends to be distorted. I tried to set up a set of nucleic acid restraints (Base pairing and base stacking for the full sequence), however, despite the fact that the syntax was checked and no error message is present in the log file, it seems that the restraints are not taken into account as if the constant restraints were two weak. And indeed when examining the refined structure, the pairing and stacking restraints for the base pairs at the extremities of the DNA duplex are not fulfilled. Have you a suggestion to solve this problem ? Thanks in advance for your help. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institute for Integrative Biology of the Cell (I2BC) UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex, France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ Web: https://www.i2bc.paris-saclay.fr [signature_2602492259]

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leave residue inside its electron density when neighbor is too close
by Murpholino Peligro 29 Jan '24

29 Jan '24

What is the recommended approach to tell phenix.refine to leave the residue inside its electron density? (crystal neighbors) The green model is the input to phenix.refine, the maps and the yellow model are the output of phenix.refine. As you can see, phenix.refine will move the residue outside the density (to avoid clashes I guess?) I have tried setting the occupancy of OXT to 0.5, but it is not good. (you can see there is a water in a special position, just above the bad residue) Any more ideas?

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phenix.mtriage output model-map
by joe.wilson2023 22 Jan '24

22 Jan '24

Dear Phenix team, I am new to Phenix and using the phenix.mtriage to get the map-model FSC results. It gives the correct results at the same time I also want to produce the mode-map used for the FSC calculation. Is there an option for this? If not how can I reproduce the same model-map with another phenix command? Many thanks, Joe

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ResolveCryoEM problem
by Luca Pellegrini 22 Jan '24

22 Jan '24

Hi, I am trying to run Resolve with two half maps and a sequence file with ncs copies of the sequence. Resolve stops with the message: “Need a symmetry file if ncs_copies > 1 and using models”. But I am not using models. Please advise. Regards, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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